For a given cancer type in the NIH Cancer Genome Atlas, I visit the data portal and download UNC RNASeqV2, level 3 expression data. Specifically, I grab files that end with the extension *.rsem.genes.normalized_results
Each file contains one line per gene, with the gene name and (I assume) its normalized FPKM expression value. I am assuming these data are normalized FPKM based on the filename and the UNC RNASeqV2 protocol description hosted on TCGA.
My questions are:
1. Are these expression data really measured in FPKM?
2. If they are, how should I convert from FPKM to TPM, for all the expression values for a given gene?
Maybe it's a little bit old, but just for future access...
@h.mon answer your second question.
For your first question: 1. Are these expression data really measured in FPKM?
Following the wiki cited by @h.mon, *.rsem.genes.normalized_results as well as *.rsem.isoforms.normalized_results have measures in normalized_count (upper quartile normalized RSEM count estimates) and not RPKM, FPKM or TPM.